Cargando…
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome r...
Autores principales: | , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2010
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851567/ https://www.ncbi.nlm.nih.gov/pubmed/20386741 http://dx.doi.org/10.1371/journal.pgen.1000891 |
_version_ | 1782179872849788928 |
---|---|
author | Nowrousian, Minou Stajich, Jason E. Chu, Meiling Engh, Ines Espagne, Eric Halliday, Karen Kamerewerd, Jens Kempken, Frank Knab, Birgit Kuo, Hsiao-Che Osiewacz, Heinz D. Pöggeler, Stefanie Read, Nick D. Seiler, Stephan Smith, Kristina M. Zickler, Denise Kück, Ulrich Freitag, Michael |
author_facet | Nowrousian, Minou Stajich, Jason E. Chu, Meiling Engh, Ines Espagne, Eric Halliday, Karen Kamerewerd, Jens Kempken, Frank Knab, Birgit Kuo, Hsiao-Che Osiewacz, Heinz D. Pöggeler, Stefanie Read, Nick D. Seiler, Stephan Smith, Kristina M. Zickler, Denise Kück, Ulrich Freitag, Michael |
author_sort | Nowrousian, Minou |
collection | PubMed |
description | Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ∼4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology. |
format | Text |
id | pubmed-2851567 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-28515672010-04-12 De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis Nowrousian, Minou Stajich, Jason E. Chu, Meiling Engh, Ines Espagne, Eric Halliday, Karen Kamerewerd, Jens Kempken, Frank Knab, Birgit Kuo, Hsiao-Che Osiewacz, Heinz D. Pöggeler, Stefanie Read, Nick D. Seiler, Stephan Smith, Kristina M. Zickler, Denise Kück, Ulrich Freitag, Michael PLoS Genet Research Article Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ∼4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology. Public Library of Science 2010-04-08 /pmc/articles/PMC2851567/ /pubmed/20386741 http://dx.doi.org/10.1371/journal.pgen.1000891 Text en Nowrousian et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Nowrousian, Minou Stajich, Jason E. Chu, Meiling Engh, Ines Espagne, Eric Halliday, Karen Kamerewerd, Jens Kempken, Frank Knab, Birgit Kuo, Hsiao-Che Osiewacz, Heinz D. Pöggeler, Stefanie Read, Nick D. Seiler, Stephan Smith, Kristina M. Zickler, Denise Kück, Ulrich Freitag, Michael De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
title |
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
title_full |
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
title_fullStr |
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
title_full_unstemmed |
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
title_short |
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
title_sort | de novo assembly of a 40 mb eukaryotic genome from short sequence reads: sordaria macrospora, a model organism for fungal morphogenesis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851567/ https://www.ncbi.nlm.nih.gov/pubmed/20386741 http://dx.doi.org/10.1371/journal.pgen.1000891 |
work_keys_str_mv | AT nowrousianminou denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT stajichjasone denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT chumeiling denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT enghines denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT espagneeric denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT hallidaykaren denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT kamerewerdjens denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT kempkenfrank denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT knabbirgit denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT kuohsiaoche denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT osiewaczheinzd denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT poggelerstefanie denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT readnickd denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT seilerstephan denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT smithkristinam denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT zicklerdenise denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT kuckulrich denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis AT freitagmichael denovoassemblyofa40mbeukaryoticgenomefromshortsequencereadssordariamacrosporaamodelorganismforfungalmorphogenesis |